Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Electronic excitations lie at the origin of most of the commonly measured spectra. However, the first-principles computation of excited states requires a larger effort than ground-state calculations, which can be very efficiently carried out within density-functional theory. On the other hand, two theoretical and computational tools have come to prominence for the description of electronic excitations. One of them, many-body perturbation theory, is based on a set of Green’s-function equations, starting with a one-electron propagator and considering the electron-hole Green’s function for the response. Key ingredients are the electron’s self-energy S and the electron-hole interaction. A good approximation for S is obtained with Hedin’s GW approach, using density-functional theory as a zero-order solution. First-principles GW calculations for real systems have been successfully carried out since the 1980s. Similarly, the electron-hole interaction is well described by the Bethe-Salpeter equation, via a functional derivative of S. An alternative approach to calculating electronic excitations is the time-dependent density-functional theory (TDDFT), which offers the important practical advantage of a dependence on density rather than on multivariable Green’s functions. This approach leads to a screening equation similar to the Bethe-Salpeter one, but with a two-point, rather than a four-point, interaction kernel. At present, the simple adiabatic local-density approximation has given promising results for finite systems, but has significant deficiencies in the description of absorption spectra in solids, leading to wrong excitation energies, the absence of bound excitonic states, and appreciable distortions of the spectral line shapes. The search for improved TDDFT potentials and kernels is hence a subject of increasing interest. It can be addressed within the framework of many-body perturbation theory: in fact, both the Green’s functions and the TDDFT approaches profit from mutual insight. This review compares the theoretical and practical aspects of the two approaches and their specific numerical implementations, and presents an overview of accomplishments and work in progress.

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Electronic excitations: density-functional versus many-body Green's-function approaches

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Principles Of Fluorescence Spectroscopy

A new hybrid density functional for general chemistry applications is proposed. It is based on a mixing of standard generalized gradient approximations GGAs for exchange by Becke B and for correlation by Lee, Yang, and Parr LYP with Hartree-Fock HF exchange and a perturbative second-order correlation part PT2 that is obtained from the Kohn-Sham GGA orbitals and eigenvalues. This virtual orbital-dependent functional contains only two global parameters that describe the mixture of HF and GGA exchange ax and of the PT2 and GGA correlation c, respectively. The parameters are obtained in a least-squares-fit procedure to the G2/97 set of heat of formations. Opposed to conventional hybrid functionals, the optimum ax is found to be quite large 53% with c=27% which at least in part explains the success for many problematic molecular systems compared to conventional approaches. The performance of the new functional termed B2-PLYP is assessed by the G2/97 standard benchmark set, a second test suite of atoms, molecules, and reactions that are considered as electronically very difficult including transition-metal compounds, weakly bonded complexes, and reaction barriers and comparisons with other hybrid functionals of GGA and meta-GGA types. According to many realistic tests, B2-PLYP can be regarded as the best general purpose density functional for molecules e.g., a mean absolute deviation for the two test sets of only 1.8 and 3.2 kcal/mol compared to about 3 and 5 kcal/mol, respectively, for the best other density functionals. Very importantly, also the maximum and minium errors outliers are strongly reduced by about 10‐20 kcal/mol. Furthermore, very good results are obtained for transition state barriers but unlike previous attempts at such a good description, this definitely comes not at the expense of equilibrium properties. Preliminary calculations of the equilibrium bond lengths and harmonic vibrational frequencies for diatomic molecules and transition-metal complexes also show very promising results. The uniformity with which B2-PLYP improves for a wide range of chemical systems emphasizes the need of virtual orbital-dependent terms that describe nonlocal electron correlation in accurate exchange-correlation functionals. From a practical point of view, the new functional seems to be very robust and it is thus suggested as an efficient quantum chemical method of general purpose. © 2006 American Institute of Physics. DOI: 10.1063/1.2148954

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Semiempirical hybrid density functional with perturbative second-order correlation

Single-reference ab initio methods for the calculation of excited states of large molecules.

The existence of Dirac cones in the band structure of two-dimensional materials accompanied by unprecedented electronic properties is considered to be a unique feature of graphene related to its hexagonal symmetry. Here, we present other two-dimensional carbon materials, graphynes, that also possess Dirac cones according to first-principles electronic structure calculations. One of these materials, 6,6,12-graphyne, does not have hexagonal symmetry and features two self-doped nonequivalent distorted Dirac cones suggesting electronic properties even more amazing than that of graphene.

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Competition for graphene: graphynes with direction-dependent Dirac cones.

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn–Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations.

https://www.pnas.org/content/pnas/114/11/2801.full.pdf

Understanding band gaps of solids in generalized Kohn–Sham theory

The form of the Kohn–Sham (KS) exchange potential, which arises from the approximation that the Hartree–Fock (HF) and the exchange-only KS determinant are equal, is derived. Two related procedures to determine the KS exchange potential follow from this approximation: a self-consistent localized HF procedure and a transformation localized HF procedure yielding the local KS exchange potential from HF orbitals. Both procedures can be considered as almost exact exchange KS methods which require only occupied orbitals and are invariant with respect to unitary transformations of the orbitals, i.e., depend only on the first order density matrix. The resulting local KS exchange potentials are free of Coulomb self-interactions and exhibit the correct long-range 1/r-behavior. The Krieger, Li, and Iafrate (KLI) procedure to determine the KS exchange potential can be considered as an approximation to the introduced localized HF procedures. Highly efficient methods to carry out the presented localized HF as well as KL...

Efficient localized Hartree-Fock methods as effective exact-exchange Kohn-Sham methods for molecules

New KS Method for Molecules Based on an Exchange Charge Density Generating the Exact Local KS Exchange Potential

The chemical bond between an adsorbed, laterally coordinated metal ion and a metal surface is affected by an additional axial ligand on the metal ion. This surface analogon of the trans effect was studied in detail using monolayers of various M(II)-tetraphenylporphyrins (MTTPs, M = Fe, Co, Zn) and their nitrosyl complexes on a Ag(111) surface. X-ray photoelectron spectroscopy (XPS) shows that the oxidation state of the Fe and Co (but not Zn) ions in the MTPP monolayers is reduced because of the interaction with the substrate. This partial reduction is accompanied by the appearance of new valence states in the UV photoelectron and scanning tunneling spectra (UPS and STS), revealing the covalent character of the ion-substrate bond. Subsequent coordination of nitric oxide (NO) to the metal ions (Fe, Co) reverses these surface-induced effects, resulting in an increase of the oxidation states and the disappearance of the new valence states. Removal of the NO ligands by thermal desorption restores the original spectroscopic features, indicating that the described processes are fully reversible. The NO coordination also changes the spin state and thus the magnetic properties of the metal ions. Density-functional theory (DFT) calculations on model systems provide structural and energetic data on the adsorbed molecules and the surface chemical bond. The calculations reveal that competition effects, similar to the trans effect, play a central role and lead to a mutual interference of the two axial ligands, NO and Ag, and their bonds to the metal center. These findings have important implications for sensor technology and catalysis using supported planar metal complexes, in which the activity of the metal center is sensitively influenced by the substrate.

Andreas Görling

Papers

Competition for graphene: graphynes with direction-dependent Dirac cones.

Understanding band gaps of solids in generalized Kohn–Sham theory

Efficient localized Hartree-Fock methods as effective exact-exchange Kohn-Sham methods for molecules

New KS Method for Molecules Based on an Exchange Charge Density Generating the Exact Local KS Exchange Potential

The Surface Trans Effect: Influence of Axial Ligands on the Surface Chemical Bonds of Adsorbed Metalloporphyrins